Murtagh pulls this on Eragon at the end of the second book of the Inheritance Cycle. The only thing Eragon can come up with to refute this assertion is along the lines of "I don't have scars on my back."
In the third book, Eragon occasionally notes how he needs to hold off on actions that would make him like Galbatorix. He doesn't really succeed, but nobody seems to notice this...
Pyramids: The Ethebian and Tsortian armies are dressed the same, fight the same, and even have the same rations they complain about. The opposing scout commanders have a pleasant conversation where they apologize to each other for the massacres they are about to enact on each other before returning to their men... and then they sheepishly turn around because they both went back to the wrong army.
Near the end of Witches Abroad, Granny Weatherwax has a Not So Different moment with her sister, Lily, who has become a Knight Templar "good" witch and the de facto ruler of Genua. Granny expresses aloud the fact that she's felt the same urges to use her powers, but never gave in to them. Earlier, Nanny and Magrat had noticed Lily saying "If you don't have respect, you don't have anything", which is a more grammatically correct version of Granny's Catch Phrase "If you ain't got respect, you ain't got nothing." Granny gives the audience a hint of her potential evil side when Lily states that she was doing a needed duty, and Granny is extremely upset that Lily apparently didn't have any fun being evil.
Not only is she annoyed that Lily didn't have fun, she is annoyed that Lily is a pathetic villain (at least in her opinion). Throughout the novel, Granny and Nanny Ogg note at various points that if Granny turned evil she would be so good at it that every evil witch that had come before her would pale in comparison. Fortunately, she subscribes to witchy ethics, and feels that because her sister ran off to be evil, she "had to be the good one" to balance things out. With Granny Weatherwax 'balance' tends to be leaning in her favor.
Subverted in Small Gods, when Brutha momentarily raises his hand as if to slap Vorbis, who calmly turns his cheek to receive the blow. Brutha hesitates, then lowers his hand, and says "I'm not like you". This really makes Vorbis — a Knight Templar who's been smugly regarding himself as a Messianic Archetype for years, and just got outclassed — pissed off.
The good version occurs in I Shall Wear Midnight, when Tiffany learns that, while she was resenting the fact that fairy tale heroines were all blonde and blue-eyed, while brown-eyed brunettes were just milkmaids, and therefore deciding to be the witch, Leticia was resenting the fact that being blonde and blue-eyed made her a fairytale princess, and therefore she couldn't be a witch. It was even the same fairy-tale book.
A more subtle Granny Weatherwax example: in A Hat Full of Sky, Tiffany asks Miss Level if Granny is the head witch, and is given the shocked reply that witches don't have leaders ... largely because Granny Weatherwax wouldn't approve. Later she asks Petulia if Anagramma is the leader of the teenage coven, and gets the same reply ... only this time it's because Anagramma doesn't approve. Given how different Granny's witchcraft is from the stuff Anagramma learnt from Mrs Earwig, this is an interesting point of similarity. (Where it goes wrong is that Anagramma and Mrs Earwig don't realise that if you're taking this tack you can't directly boss other witches around, at least not too much.)
In Night Watch Vimes recognises Carcer as what he might have become with a different upbringing.
In President's Vampire, Konrad tries to convince Cade of this, but it's quickly pointed out that while both kill people, Konrad does it for his sick experiments, and Cade does it to protect others. Not to mention that Cade doesn't really make it to the end of Konrad's Breaking Speech, instead performing a Shut Up, Hannibal! by the way of almost ripping off his head.
In Good Omens, made quite clear that Heaven and Hell are Not So Different. Demons in the book are former angels after all, and have the same feathery wings, albeit somewhat better groomed.
In Black Legion, after Mind Raping Telemachon into doing his will, Khayon realizes that this makes him just like Ahriman, who did this to nearly half of the Thousand Sons, turning them into Rubrics. As Khayon was the lead opponent of the Rubric curse, this makes him more than a bit disturbed.
In The Lord of the Rings, Sam wonders of the dead Southron soldier "whether he was really evil at heart, and what lies or threats had driven him on this march so long from his home, and whether he would have rather stayed there in peace."
A speech given to Faramir in film, but omitted from the theatrical movie, presumably because it was felt to be Too Soon after 9/11.
"I wish Merry was here," he heard himself saying, and quick thoughts raced through his mind, even as he watched the enemy come charging to the assault. "Well, well, now at any rate I understand poor Denethor a little better. We might die together, Merry and I, and since die we must, why not?"
"But I say to you, King of the Númenóreans, not till now have I understood the tale of your people and their fall. As wicked fools I scorned them, but I pity them at last. For if this is indeed, as the Eldar say, the gift of the One to Men, it is bitter to receive."
The Silmarillion and supporting materials mention that the Ainur Aulë and Sauron were very similar in the beginning, both being interested in artifices and engineering and both being impatient that the Children of Ilúvatar (Elves and Men) had not yet awoken. The difference is that when both were given a chance to repent, Aulë did so and Sauron did not.
Galadriel also explicitly compares herself to Sauron; a powerful being who proudly rejected the Valar's invitation to the Undying Lands, and desires to preserve their realm and power against the slow changes of the world.
The Reynard Cycle: Upon being told that the Calvarians committed a racially motivated genocide upon the people of Solothurn, Cointereau says that their entire race should be wiped from the world for doing such a thing. Isengrim, a Calvarian, points out the hypocrisy of the statement.
"A Knight's a sword with a horse. The rest, the vows and the sacred oils and the lady's favors, they're silk ribbons tied 'round the sword. Maybe the sword's prettier with ribbons hanging of it, but it'll kill you just as dead. Well, bugger your ribbons, and shove your swords up your arses. I'm the same as you. The only difference is, I don't lie about what I am. So, kill me, but don't call me a murderer while you stand there telling each other your shit don't stink. You hear me?"
Also comes up with the various feudal states, unsurprisingly for a book about medieval Realpolitik. Slavery is common in Essos while Slavery Is a Special Kind of Evil just over the ocean in Westeros and in the Iron islands. However the nobility of Westeros impose crippling class oppression on the "smallfolk" (peasants), who effectively belong to whatever lord claims the land they live on (which can change due to circumstances such as conquest, marriage or royal decree) and can face losing limb or life for trivial slights against their lords, while the Ironborn look down on chattel slavery but taking "thralls" (indentured labourers whose children will be freemen) and "salt wives" (female captives) from raids is fair game. As noted by Tyrion Lannister in his travels through Essos, many slaves are treated better than the Westerosi peasantry, and being a peasant in Westeros is often being a slave in all but name. In other words, the peoples of this world cling to notions of civilisation through trivial linguistic gymnastics.
An uneasy dynamic between Harry Potter and Voldemort, made most explicit in the second book. They have similar appearances (at least with Voldemort's past self), abilities, passions, disregard for rules (although Harry's father James was also shown to have a similar disregard for the rules in his youth, so it may have also been from his father as well), and histories. As well, some of Voldemort's power was transferred to Harry at the beginning of the first book, and at the end of the fourth book, Voldemort transfers some of Harry's motherly protection to him.
This trope is very nearly mentioned by name in Deathly Hallows, when Harry finally sees all of the parallels between himself, Voldemort, and Severus Snape.
Justified, however, in that Harry has had a piece of Lord Voldemort's soul resident inside his body ever since he was a year old.
Nearly every Animorphs book explores this theme, with the Animorphs worrying that they are becoming too ruthless, too willing to do anything they have to in order to win their war. And they compare themselves to the Yeerks, who are paragons of ruthlessness. The characters face many morally ambiguous situations, which either dispel or (perhaps more often) confirm these doubts. Some Yeerk characters have made "not so different" arguments to the Animorphs, especially Karen/Aftran, Taylor, and the human villain David.
In "The Message" Cassie feels that it's wrong to morph a dolphin - an animal that's intelligent. She raises the question of how morphing is different then what the Yeerks do.
"It will be strange morphing something so intelligent," Rachel said. "Yes," I agreed. "Strange, and . . . wrong, somehow. I felt a twisting in my stomach. "How is doing this any different than what the Yeerks do?" Rachel looked surprised. "Yeerks take over humans," she said. "Besides, they don't morph, they infest. We don't take over the actual animal, we just copy his DNA pattern, create a totally new animal, and then - " "And then control the new animal," I said. "It's not the same," Rachel insisted. But she looked troubled. "It's something I'll have to think about," I said. "It's kind of been bothering me."
Also done with the Howlers and the Pemalites, two alien species created by Crayak and the Ellimist. The Howlers look like Always Chaotic Evil who kill everything in their path and the Pemalites are insanely pacifistic, but the two races, thanks to how they were designed, actually had the exact same priority in life: to have fun. Their creators just gave them different ideas of 'fun'.
A major part of the series was Jake becoming increasingly ruthless. By the end, it's impossible to ignore the parallels between him and Alloran. Even aside from their actions, there are similarities in their circumstances, as both of them had a brother they were forced to fight - Jake because Tom had been infested, and Alloran because he himself had been infested.
Fevre Dream, Damon Julian saying the "We are not so different" to Abner Marsh. Abner actually agrees with him, but still refuses to Julian's We Can Rule Together.
In the later books in A Series of Unfortunate Events, the Baudelaires are almost paralyzed a few times from the idea that by lying and wearing disguises everywhere, they're starting to become like Olaf and his gang. This particularly surfaces in The Grim Grotto, wherein they discover one of the gang - the Hook-Handed Man - is in fact the older brother of one of their newest friends, driven to villainy by his tragic past. He himself explains it:
"People aren't either wicked or noble," the hook-handed man said. "They're like chef's salad, with good things and bad things chopped and mixed together in a vinaigrette of confusion and conflict."
In this particular case, however, the example is subverted. The hook handed man claims that VFD is as bad as the villains, but the Baudelaires consider it and refute this, deciding that while VFD may have made morally questionable decisions, ultimately the difference is that one side starts fires and the other side puts them out.
As the Baudelaires slowly became more wary of their 'villainous' deeds over the course of the plot, Olaf and his associates were gradually either killed off or - especially in the case of Olaf himself, in his final moments - found to have a hidden 'human' side. Asked about the subject, the author (Daniel Handler) commented:
"It's sad, isn't it? I think the Baudelaires are getting older, and one of the sad facts about getting older is that you've always thought of yourself and people you know as righteous and true and the people you dislike as evil. The older you get the more muddy that water becomes."
In Mere Christianity, a theological work by C. S. Lewis, the writer subverts the tradition by pointing out that if British were really so different from Nazis there would be no point in being horrified; because there would in fact be nothing to judge them on. That is they could not say their enemies were evil or that British were less bad then Nazis unless there actually was enough in common to judge them.
The Big Bad of The Thief of Always tries to pull this on the hero, pointing out that although the Big Bad was a soul-stealing monstrosity, the Hero remorselessly killed the Big Bad's minions, who weren't willfully evil, at least one of whom wasn't hostile, and who were thoroughly convincing and seemingly "real", despite actually being dust given life with illusion. The hero doesn't so much counter it as just shrug it off and continue trying to take down the Big Bad — because, well, the Big Bad is a soul-stealing monstrosity who, despite his valid points, is not the least bit sympathetic and who absolutely has to be destroyed.
Hood is correct in this assessment; they've both stolen things that make a person what they are — things that should never be taken by anyone. Hood has stolen the souls of the children lured to his Holiday House, while Harvey has stolen the lives of Hood's illusory minions. The difference comes in why they did it — Harvey did it to lure out Hood so he could defeat him and save the children trapped there, while Hood has merely done it to extend his warped existence and feed his unholy hunger. The book is showing that the difference between heroism and villainy sometimes isn't in what you do, but why you do it. Not the sort of thing you tend to see in a children's book.
Ratha of The Book of the Named bit and crippled her cub, Thistle-chaser. Years later, Thistle-chaser comes back for revenge against Ratha. A small cub tries to defend her, and Thistle-chaser knocks it out of the way. Ratha tells Thistle-chaser that she is no different than herself, since Thistle-chaser got between her and her true target.
Jenny and Julian, from L. J. Smith's The Forbidden Game trilogy, could be said to fit this trope. There's a part of the seemingly-timid Jenny which likes danger and challenge, and a part of Julian that is surprisingly different from the others of his 'family,' and seems to long for things that don't fit his projected personality. If brought up in the same place, they might've been uncannily similar people.
Zhi Zhong in the Conqueror books occasionally catches himself admiring Genghis Khan's ambition and tactical prowess, comparing his enemy to himself. Jelaudin later ponders on how his father used tactics very similar to Genghis in his own wars.
Used as a theme in Neil Gaiman short story A Study In Emerald, which is a crossover between Sherlock Holmes and the Cthulhu Mythos. (And no, I'm not kidding.) Here there is a detective who lives on Baker Street and is aided by his housemate/war veteran friend. Said detective investigates crimes, often at the behest of Inspector Lestrade of Scotland Yard. Only at the very end of the story does it become increasingly clear that the detective is in fact Professor James Moriarty, (and that the war veteran is Moriarty's right hand man Colonel Sebastian Moran) while the criminals/rebels being hunted are Sherlock Holmes and Dr Watson.
In Simon Spurrier's Warhammer 40,000Night Lords novel Lord of the Night, Mira realizes this about her and Saheel on her own. Indeed, reflecting on how similar their personalities were led her to consider that the Imperium had not treated her well. She still resisted in their climatic confrontation — but not forever. Considering the Imperium, whether this is corrupting her is an open question.
In Red Dragon, deranged-but-brilliant serial killer Hannibal Lecter loves to tweak FBI profiler Will Graham with this idea whenever they interact, face-to-face or through mail. It isn't clear how much of it Lecter himself believes, but that disturbing knack he has for empathizing with and thinking like the psychopaths he chases is oh-so-much-fun to play with! Lecter has a similar relationship with Starling in The Silence of the Lambs; they are frequently compared and in his letter to her at the end of the book he makes this explicit:
Lecter: "Some of our stars are the same, Clarice."
Warrior Cats: The majority of the plot for the second half of The New Prophecy is about how similar Brambleclaw is to Hawkfrost and how they are, in turn, like their father. Firestar has also been compared to Tigerstar (since they are both somewhat ambitious) and Scourge (Since they are unknowingly related, and the author's note at the beginning of Rise of Scourge talks about how the author wanted to take a character born with the same gifts as Firestar and give him a more negative upbringing).
In John le Carr? Smiley's People, the ostensibly retired British spy George Smiley finally gets a chance to beat the Soviet spymaster Karla, using the knowledge of a mentally ill daughter hidden in an institution in Switzerland against him. He succeeds, forcing Karla to defect and tell everything he knows to the Brits. But he gains no satisfaction in the end, because he feels he has finally gone over the line and become as ruthless as Karla to beat him.
In the X-Wing Series, Kirtan Loor is left behind on Coruscant when the Empire leaves it, recently infected with a nasty plague, to the New Republic. He's instructed to make things difficult for the New Republic, and he does this with gusto, using agents and explosives to make people balance dying of the Krytos virus with being blown up at a health center. Vorru is sent to hunt him down, but instead of bringing him to justice he uses Loor to further his own ends, giving him targets to take out. One of them is a school. When Loor protests, Vorru mocks him. Loor is already preventing children from being treated; just because it's the Krytos virus and not him who is killing them makes no difference. Loor agrees because Vorru will kill him otherwise, but thinks, We are not as far apart as I would like to think, but neither are we as close as Vorru thinks. He also felt his tactics were not so different from those of the Rebels, who have now taken over the planet and become the government—i.e. a small insurgent force launching attacks on the more powerful state. The Rebels however never resorted to simple terrorism, unlike him.
Magic: The Gathering novels: the second book of the Invasion cycle, Planeshift, has Urza and Yawgmoth, Gerrard Capashen and Crovax, and Phyrxians and Metathran.
In John C. Wright's The Golden Transcendence, the Silent Oecume agents try this on Phaethon who sees through it. (They complain that AI's don't obey orders. Phaethon wonders why they didn't just fire them and hire new ones — and knows it's because they enslaved them.) Both Phaethon and Helion have this reaction more than once to Atkins, which neither finds entirely pleasant, but they have to admit it's accurate.
In Allison Croggon's fantasy series, the Books of Pellinor, the main character Mearad is constantly wondering whether she is good or evil at heart because of the similarities between her and the Big Bad, Sharma- The Nameless One.
The whole point of Animal Farm. In the story, the farm animals kick the humans out and take over their farm. They establish a set of rules to keep them from associating with humans (among the rules were no sleeping in beds, no wearing clothes, no drinking, no walking on hind legs, etc.). Napoleon, a pig, is more concerned about the welfare of himself and his fellow pigs than the other animals. Over time, the pigs start indulging in more and more human luxuries, and mannerisms, all while continuing to exploit the other animals, until the famous end scene where Benjamin the donkey sees the pigs drinking and hanging out with men, and he's unable to tell the difference between the pigs and the men. The whole story was symbolism for how author George Orwell interpreted Communist Russia: the leaders just exploited the workers for their own gain, effectively making them the same as the aristocratic upper class communism sought to overthrow.
In The Voyage of the Jerle Shannara The Morgawr hits his former apprentice, the Isle Witch with this, noting that she is every bit as dark, twisted and ruthless as he is. The Isle Witch acknowledges his point, admitting the only difference between them is that she regrets what she is and would change it if she could, while The Morgawr regrets nothing.
In Aquasilva Trilogy, the main character Cathan and his arch enemy Sarhaddon end in the same side of the trench. They were both trying to avoid a bloody war, albeit with different motivations. Cathan wanted to destroy the Domain altogether and Sarhaddon, being a part of said Domain, fears that a new war would be the downfall for his organization. In the end, Sarhaddon was right.
In Darkness at Noon, Ivanov tells Rubashov that their positions could easily have been reversed, and Rubashov admits to himself that, because they shared the same philosophy, if he had been interrogating Ivanov he would have brought the same arguments against him. This is one likely reason why Ivanov is also arrested and shot.
In Väinö Linna's The Unknown Soldier Major Sarastie of Lt. Col Karjula: Those people who without the army would be either prison wardens or criminals. Only pure chance at start would decide, which side of the bars he'd be looking at.
Rand and Ishamael/Moridin in The Wheel of Time. Both of them began as idealists and both found themselves driven to despair by a world of Eternal Recurrance and reincarnation where nothing ultimately seemed to be able to change except for the constant threat of the Dark One trying to destroy reality, and both teetered on the edge of nihilism. Except that Rand came to the realization that Eternal Recurrance and reincarnation exists to give people an infinite opportunity to redeem themselves from their mistakes and dedicates himself to protecting the world; Ishamael embraced nihilism completely and dedicated himself to the Dark One's service in order to put reality (and himself) out of its misery.
In Redeeming Love, the heroine—a former prostitute—is engaged in a conflict with her brother-in-law throughout the novel that mostly stems from their understanding of this trope. He knows he doesn’t have the moral high ground, but is too ashamed of his own hypocrisy to admit it; she loathes him for trying to stomp her into the dirt for her past immorality when he’s done things that are just as wrong—by today’s standards, even more wrong—than she has (primarily blackmailing her into sleeping with him when she had already married his brother). They work it out…eventually, once he realizes she’s really reformed (by The Power of Love) and she is able to forgive him.
In Waverley the hero comments that an English prisoner he meets and a Jacobite highlander are rather alike in their dislike for each other's culture and politics.
In Douglas Hulick's Among Thieves, Drothe, the main character, is captured and held at daggerpoint by a Sash (the Emperor's elite guards). In a (successful) attempt to anger her enough to let her guard down so he can escape, he tells her that her cunning in capturing him reminds him greatly of the sort of scheming his criminal friends might employ, and that if she ever tires of her life as a Sash, he could probably get her a job in his organization.
In Ruth Frances Long's The Treachery of Beautiful Things, the piper does not realize he is using this trope when he tells Jenny that Jack has nothing common with them. She spits back that she's nothing like him, and neither is Jack, and aren't they blessed in that?
In the Doctor Who Expanded Universe novel The Silent Stars Go By, the Doctor sharply contrasts the human colonists (Morphans) on Hereafter, who are working hard to terraform the planet in the knowledge that eventually their descendants will benefit, with the Ice Warriors, who plan to alter the terraforming machinary to suit their own needs, then hibernate until it's ready for them. It turns out the Morphans aren't preparing the planet for their descendants but their ancestors, who are in cryo-sleep beneath the terramorphing engines. It also turns out some of them have woken up, and the horrible red-eyed monsters preying on the colonies aren't the Ice Warriors.
The Hunger Games: In the film, Foxface briefly bumps into Katniss whilst running from the Cornucopia bloodbath, and the look of terror she wears is a reflection of Katniss's own fear.
In Dinner at Deviant's Palace the villain suggests this to the hero near the end, that they're both basically selfish and only interested in other people for what can be taken from them, while offering him a We Can Rule Together. The hero has gained enough self-awareness during his quest to calmly admit that the villain has a point, but also to know that the quest has changed him and that although he may not be much different, it's enough to matter.